Mixed in with the microfilters, GPS units and conductivity monitors on last week’s National Science Foundation river survey were eight red-capped plastic soda bottles. Project principal investigator Marc Peipoch of the University of Montana made sure they were in easy reach in his canoe.

“You can spend money on gear or you can buy Coke,” Peipoch said. “This is the best gas-tight bottle you can find.”

Replace the soda with river water, and a geoscientist can determine the age of radon gas isotopes dissolved within. Radon gas signifies underground water, and its isotopes slowly decay over about four days’ exposure to sunlight. Knowing the gas condition gives hints about the mix of ground water and surface water flowing in the Clark Fork River.

At its headwaters just east of Anaconda, the Clark Fork looks like any pastoral stream. Just a couple dozen feet wide and a few feet deep, it writes a cursive script through the Deer Lodge Valley next to Interstate 90. An attentive motorist might notice a lot of earth-moving going on in its floodplain.

That’s because in 1908, a catastrophic flood tore through the mine tailings of Butte and Anaconda and deposited lethal amounts of arsenic, copper and other metals throughout the drainage. The surge nearly ripped out brand-new Milltown Dam just east of Missoula. The dam held, and that’s where several million tons of heavy metal sludge came to rest in its reservoir.

Lots more got deposited in oxbows all along the Deer Lodge Valley. Known as slickens, these poisoned riverbanks remained virtually sterile for a century. Mining cleanup efforts between Butte and Missoula formed the largest contiguous federal Superfund site in the nation.

A lot of the big-ticket work grew out of settlements between the legacy mining owners and the state and federal government. Those agreements provided millions of dollars for removal of Milltown Dam, reconstruction of Silver Bow Creek through Butte, and numerous other smaller projects throughout the drainage.

Today, most of the upper Clark Fork work depends on the Montana Department of Environmental Quality for removal of the remaining toxic metals, and the Department of Justice’s Natural Resource Damage Program for restoration of the resulting ecosystem. They’re working from a $96 million trust fund paid by the mining companies to repair damage to the 47-mile upper reach of the Clark Fork.

To do that, we have to know how the upper Clark Fork should behave if it hadn’t endured a century of abuse. That requires lots of scientific detective work.

“The upper Clark Fork is a sleeping giant of a fishery,” said Will McDowell of the Clark Fork Coalition, a Missoula-based river conservation group. “It has natural productivity, probably tied to those natural nutrient sources. If it was otherwise healthy, it could be a tremendous fishery. There’s no reason it shouldn’t be, except for the metals.”

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The Natural Resource Damage Program (NRDP) sees the upper Clark Fork in three segments: headwaters to Drummond, Drummond to Rock Creek, and Rock Creek to Bonner. That middle reach has the worst fishery conditions, but the upper end might be the source of the problem. Removing the heavy metals will have a big impact, but that leaves the nutrient load in search of answers.

“We want to know why is the green algae in that stretch from Drummond to Rock Creek so prominent?” said NRDP’s Doug Martin. “And if possible, how to fix it? What’s the limiting factor? Is there something we could do or some way to use our restoration funds?”

But rivers are giant, moving chemistry sets, and the upper Clark Fork presents some remarkable puzzles. For example, phosphorus has a huge impact on plant growth in rivers. Add too much and it works like fertilizer that gooses plant growth, which consumes all the oxygen in the water and kills the fish.

Phosphorus can come from things like cleaning products, which is why places like Missoula participated in campaigns to use non-phosphate-based laundry detergent to improve water quality. But it also occurs naturally, as any I-90 motorist driving by the Phosphate exit near Garrison might realize. That commemorates the last underground phosphate mine in the United States, which closed in 1993.

The other major nutrient in a river system is nitrogen. Those who remember their earth science classes recall the frustratingly complex nitrogen cycle of phases the element goes through as it builds up and breaks down in living systems. University of Montana systems ecologist Maury Valett suspects that cycle is misfiring in the upper Clark Fork, jerking its plant and animal life in awkward directions.

“This river is way greener than it should be,” Valett said. The state has set up a 15-phase project to remove the mining metals from the upper Clark Fork and restore its floodplain to a more natural condition. But that assumes we know what natural looks like.

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Valett and Peipoch have a five-year, $450,000 National Science Foundation grant to help the state agencies learn what that chemistry should be. They’ve combined with funding from state agencies to make sense out of huge collections of data developed over the years of restoration work on the river.

And in the upper Clark Fork kitchen, lots of chefs stir the pot. The Warm Springs Ponds just above its headwaters were built to catch mining waste flowing down from Butte in Silver Bow Creek. They remove lots of copper, and also trap a great deal of nitrogen. But they also release arsenic downstream, and they interfere with water temperature and flooding cycles that other parts of the nitrogen cycle depend on.

Then there’s human activity, including the sewage treatment plants at Butte and Anaconda and Deer Lodge, the septic systems of the surrounding ranches, and the fertilizer applied to the farm fields. There’s acres of cow manure that both absorbs and releases different forms of nitrogen as it gets plopped onto and plowed into the soil. There’s even a possibility that the decades of ammonium-based explosives used in digging Butte’s open-pit copper mine might be contributing residual nitrogen to the system.

And don’t forget the natural world. Valett and Peipoch can tell to some degree where the nitrogen compounds in the water come from. And a surprising amount bears chemical signatures of soil bacteria. That hints at the activity of wetlands full of microorganisms decomposing organic matter and turning it into nitrogen fertilizer.

“That’s why we need a bunch of boats and a bunch of bottles,” Valett said. On a water-sampling float last November, a series of test sites showed virtually no nitrogen until one spot where it seemed to come in through a fire hose. But there was no “smoking gun” of a sewer pipe or irrigation ditch to produce the spike. Furthermore, the nitrogen was flowing in winter, when those microorganisms are typically too cold to digest anything.

Conversations with mining historians hint at a possible ancient, underground wetland near Anaconda that might be insulated enough to function better in winter than in summer, when much of its groundwater gets drawn away for irrigation. But that’s just a guess. It will take multiple floats down the river to determine where the nutrients come from and how to bring them into balance.

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It takes just six minutes for a freeway driver to cover the distance between Warm Springs and Racetrack. A canoeist needs about seven hours of constant paddling to get through the 11 miles of curlicue curves packed between those two exits. The UM sampling crews plan to float that reach several times a year.

Of course, that counts the time needed to take new samples every 500 meters, to check every tributary stream for its water signature, and to escape the occasional entanglement with low-hanging willow bushes. The upper section of the river is closed to public floating because of all the restoration and remediation work along its banks. That makes it a haven for nesting geese and ducks, muskrats and beavers, and the occasional tail-slapping brown trout.

“This is fun science,” Valett said. “It’s a chance to preserve and improve some of things Montana is known for. We’re trying to help the landscape make sense. It’s complicated as hell, but most good problems are.”